Local neutral networks help maintain inaccurately replicating ribozymes.

PubWeight™: 0.77‹?›

🔗 View Article (PMC 4192543)

Published in PLoS One on October 09, 2014

Authors

András Szilágyi1, Ádám Kun2, Eörs Szathmáry3

Author Affiliations

1: Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany; MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary.
2: Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany; MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary.
3: Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany; MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary; Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary.

Articles citing this

Evolution of the division of labor between genes and enzymes in the RNA world. PLoS Comput Biol (2014) 0.83

Articles cited by this

(truncated to the top 100)

Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften (1971) 13.09

From sequences to shapes and back: a case study in RNA secondary structures. Proc Biol Sci (1994) 6.01

RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science (2001) 4.53

Neutral evolution of mutational robustness. Proc Natl Acad Sci U S A (1999) 4.38

The antiquity of RNA-based evolution. Nature (2002) 4.26

Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res (2002) 4.16

Directed evolution of an RNA enzyme. Science (1992) 3.68

Ribozyme-catalyzed transcription of an active ribozyme. Science (2011) 3.42

A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl Acad Sci U S A (2003) 3.28

Directed evolution of nucleic acid enzymes. Annu Rev Biochem (2004) 3.27

RNA-catalysed nucleotide synthesis. Nature (1998) 2.80

Retracted Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol (2005) 2.77

Group selection of early replicators and the origin of life. J Theor Biol (1987) 2.63

In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity. Nature (2002) 2.08

Statistics of RNA secondary structures. Biopolymers (1993) 2.06

Peptide bond formation by in vitro selected ribozymes. Nature (1997) 2.05

Real ribozymes suggest a relaxed error threshold. Nat Genet (2005) 2.00

Structure and function of the hairpin ribozyme. J Mol Biol (2000) 1.98

Error thresholds of replication in finite populations mutation frequencies and the onset of Muller's ratchet. J Theor Biol (1989) 1.76

RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res (1996) 1.72

A small catalytic RNA motif with Diels-Alderase activity. Chem Biol (1999) 1.70

Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers (2007) 1.66

Automated selection of anti-protein aptamers. Bioorg Med Chem (2001) 1.60

Aptamer database. Nucleic Acids Res (2004) 1.60

Stationary mutant distributions and evolutionary optimization. Bull Math Biol (1988) 1.56

Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3. Proc Natl Acad Sci U S A (2003) 1.54

A tetracycline-binding RNA aptamer. Bioorg Med Chem (2001) 1.52

In-ice evolution of RNA polymerase ribozyme activity. Nat Chem (2013) 1.52

Structural diversity of self-cleaving ribozymes. Proc Natl Acad Sci U S A (2000) 1.44

Selection in vitro of novel ribozymes from a partially randomized U2 and U6 snRNA library. EMBO J (1998) 1.43

RNA aptamers specifically interact with the prion protein PrP. J Virol (1997) 1.43

Specific, rapid synthesis of Phe-RNA by RNA. Proc Natl Acad Sci U S A (1999) 1.42

A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA (1999) 1.36

Altering molecular recognition of RNA aptamers by allosteric selection. J Mol Biol (2000) 1.34

Inhibition of rat corneal angiogenesis by a nuclease-resistant RNA aptamer specific for angiopoietin-2. Proc Natl Acad Sci U S A (2003) 1.32

In vitro RNA random pools are not structurally diverse: a computational analysis. RNA (2005) 1.32

Automated RNA selection. Biotechnol Prog (1999) 1.27

RNA-Catalyzed CoA, NAD, and FAD synthesis from phosphopantetheine, NMN, and FMN. Biochemistry (2000) 1.27

The limits of specificity: an experimental analysis with RNA aptamers to MS2 coat protein variants. Mol Divers (1999) 1.25

Replication and mutation on neutral networks. Bull Math Biol (2001) 1.21

Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J Am Chem Soc (2010) 1.21

In vitro selection of RNA molecules that inhibit the activity of ricin A-chain. J Biol Chem (2000) 1.20

RNAs that bind and change the permeability of phospholipid membranes. Proc Natl Acad Sci U S A (1999) 1.20

RNA-catalyzed thioester synthesis. Chem Biol (2002) 1.18

Prebiotic replicase evolution in a surface-bound metabolic system: parasites as a source of adaptive evolution. BMC Evol Biol (2008) 1.18

Selective targeting and inhibition of yeast RNA polymerase II by RNA aptamers. J Biol Chem (1997) 1.17

Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res (2005) 1.17

The robustness of naturally and artificially selected nucleic acid secondary structures. J Mol Evol (2004) 1.17

Phenotypic error threshold; additivity and epistasis in RNA evolution. BMC Evol Biol (2005) 1.17

An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res (2003) 1.15

RNA-catalyzed amino acid activation. Biochemistry (2001) 1.15

RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry (1996) 1.14

Rapid and simple ribozymic aminoacylation using three conserved nucleotides. J Am Chem Soc (2009) 1.13

In vitro selection and characterization of streptomycin-binding RNAs: recognition discrimination between antibiotics. RNA (1998) 1.13

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)(a). Biol Direct (2012) 1.12

Isozyme-specific inhibition of protein kinase C by RNA aptamers. J Biol Chem (1994) 1.10

An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J (2001) 1.10

Selection of novel Mg(2+)-dependent self-cleaving ribozymes. EMBO J (1995) 1.09

RNA aptamers to S-adenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S-adenosylhomocysteine antibody. Biochemistry (2000) 1.05

Isolation of novel ribozymes that ligate AMP-activated RNA substrates. Chem Biol (1997) 1.04

The roads to and from the RNA world. J Theor Biol (2003) 1.04

A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III-IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId. Nucleic Acids Res (2005) 1.03

Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease. Eur J Biochem (2000) 1.03

A novel ribozyme with ester transferase activity. Chem Biol (1998) 1.03

Molecular recognition of cAMP by an RNA aptamer. Biochemistry (2000) 1.03

Activation of 2'-5' oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers. J Biol Chem (1998) 1.02

23S rRNA similarity from selection for peptidyl transferase mimicry. Biochemistry (1997) 1.02

In vitro selection of self-cleaving RNAs with a low pH optimum. Proc Natl Acad Sci U S A (1997) 1.02

Novel RNA catalysts for the Michael reaction. Chem Biol (2001) 1.01

A ribozyme for the aldol reaction. Chem Biol (2005) 1.00

In vitro selection of RNA molecules that displace cocaine from the membrane-bound nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (1998) 1.00

RNA molecules that bind to and inhibit the active site of a tyrosine phosphatase. J Biol Chem (1998) 0.99

Acyl-CoAs from coenzyme ribozymes. Biochemistry (2002) 0.99

Ribozyme-catalyzed aminoacylation from CoA thioesters. Biochemistry (2005) 0.98

Selection and stabilization of the RNA aptamers against the human immunodeficiency virus type-1 nucleocapsid protein. Biochem Biophys Res Commun (2002) 0.97

Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA (2000) 0.96

RNA aptamers to mammalian initiation factor 4G inhibit cap-dependent translation by blocking the formation of initiation factor complexes. RNA (2006) 0.96

RNA aptamers as pathway-specific MAP kinase inhibitors. Chem Biol (2000) 0.96

Detecting immobilized protein kinase C isozymes with RNA aptamers. Anal Biochem (1996) 0.96

In vitro selection of a 7-methyl-guanosine binding RNA that inhibits translation of capped mRNA molecules. Proc Natl Acad Sci U S A (1997) 0.95

In vitro selection of adenine-dependent hairpin ribozymes. J Biol Chem (2003) 0.95

Isolation of RNA aptamers specific to the NS3 protein of hepatitis C virus from a pool of completely random RNA. Virology (1997) 0.94

A more complex isoleucine aptamer with a cognate triplet. J Biol Chem (2005) 0.94

RNA aptamers that specifically bind to a 16S ribosomal RNA decoding region construct. Nucleic Acids Res (2000) 0.93

Targeting the variable surface of African trypanosomes with variant surface glycoprotein-specific, serum-stable RNA aptamers. Eukaryot Cell (2003) 0.93

5'-RNA self-capping from guanosine diphosphate. Biochemistry (1997) 0.93

The evolution of enzyme specificity in the metabolic replicator model of prebiotic evolution. PLoS One (2011) 0.92

Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function. Eur J Biochem (1998) 0.91

In vitro selection of allosteric ribozymes: theory and experimental validation. J Mol Biol (2001) 0.91

Anti-(Raf-1) RNA aptamers that inhibit Ras-induced Raf-1 activation. Eur J Biochem (2002) 0.90

In vitro selection of the RNA aptamer against the Sialyl Lewis X and its inhibition of the cell adhesion. Biochem Biophys Res Commun (2001) 0.89

High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. Nucleic Acids Res (2002) 0.89

High-affinity aptamers to subtype 3a hepatitis C virus polymerase display genotypic specificity. Antimicrob Agents Chemother (2006) 0.88

Aptamers that bind to the antibiotic moenomycin A. Bioorg Med Chem (2001) 0.86

Aptamer selection for the inhibition of cell adhesion with fibronectin as target. Bioorg Med Chem Lett (2004) 0.85

Anti-idiotype RNA selected with an anti-nuclear export signal antibody is actively transported in oocytes and inhibits Rev- and cap-dependent RNA export. Proc Natl Acad Sci U S A (1997) 0.85

In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. Biochemistry (2004) 0.85

In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide. RNA (1996) 0.85

High-affinity aptamers selectively inhibit human nonpancreatic secretory phospholipase A2 (hnps-PLA2). J Med Chem (1998) 0.84

Motif frequency and evolutionary search times in RNA populations. J Theor Biol (2011) 0.83